Well it might have something to do with the player's personality and media handling style. My Balotelli is just one problem after another. First he refuses to train hard, and then he just starts to hate Silva. So I think violate players have more of a chance to hate.
Although this isn't the case in what you're talking about I've noticed this problem can also come from tutoring players. I had Fabio tutoring one of my younger right-backs and now they hate each other.
If they have different personalities they can start disliking each other when tutoring. But when it happened to me (only once I think) it all get back to normal after some time (after the tutoring stopped).